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MOLBIO LEC > Unit 7 > Flashcards

Unit 7 Flashcards

1
Q

MOLECULAR DIAGNOSIS OF INFECTIOUS DISEASES

A

Infectious diseases involve:
○ Viruses
○ Bacteria
○ Fungi
○ detect parasites

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2
Q
  1. Molecular characterization of microorganisms.
  2. Development and evaluation of molecular-based laboratory tests of clinical specimens isolated in cultures.
  3. Comparison of biochemically similar organisms in outbreak situations (known as molecular epidemiology) to ascertain whether the isolates have a common independent source.
A

APPLICATIONS OF MOLECULAR TECHNOLOGY

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3
Q

APPLICATIONS OF MOLECULAR TECHNOLOGY

A
  1. molecular characterization
  2. for molecular based laboratory tests
  3. molecular epidemiology
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4
Q

Comparison of biochemically similar organisms in outbreak situations is known as?

A

molecular epidemiology

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5
Q

Example of molecular epidemiology

A

SARSCOV (alpha, beta, delta, and omicron strains), slightly different genomes

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6
Q

Analyte for molecular testing used in PCR, RT-PCR, LAMP etc.

A

genome

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7
Q

mRNA transcript (basis for gene expression)

A

Transcriptome

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8
Q

proteins of an organism (this is not targeted by molecular tests as much as genome)

A

Proteum

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9
Q

Proteum is used in which detection method?

A

MALDI-TOF (Laser desorption targets protein»ionizes»charged)

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10
Q

Pure culture/colony is used in MALDI-TOF

A

TRUE (ie proteum)

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11
Q
  1. Time-consuming to isolate organisms
  2. Hazardous with which to work in the clinical laboratory
  3. Reliable laboratory tests were lacking
  4. Organisms that are received in clinical laboratories in high volumes
  5. Genes that confer resistance to antimicrobial agents
  6. Characterization of DNA, RNA, and protein to find and identify new organisms and to further characterize or classify known organisms.
A

COMMON SPECIFIC TARGETS

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12
Q

Hazardous with which to work in the clinical
laboratory

A

systemic fungi (histoplasma/coccidioides); dangerous to grow in the lab kaya mas safer if molecularly tested

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13
Q

Time-consuming to isolate organisms

A

TB = takes 8 weeks to be isolated

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14
Q

Reliable laboratory tests were lacking

A

Hepatitis C
■ Culturing viruses in laboratories is
impractical and costly
■ Can be detected through genomic
testing, protein testing
(antigen/antibody testing)

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15
Q

Organisms that are received in clinical laboratories in high volumes

A

Streptococcus pyogenes, Chlamydia trachomatis, neisseria gonorrhoeae (last
two often undergo PCR in the Philippines)

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16
Q

ginagamit for transport and collection of swab sample dahil mas maliit yung swab nya; less painful

A

Stuart transport medium

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17
Q

Genes that confer resistance to antimicrobial agents

A

Methicillin-, Oxacillin-, Vancomycin-resistant

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17
Q

VRSA Genes

A

Van A, Van B, Van C, enterococcus
resistance to vancomycin

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18
Q

MRSA Gene

A

mecA and mecC

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19
Q

■ Staphylococcus
■ Klebsiella
■ Acinetobacter
■ Pseudomonas
■ Enterococcus
1. E. faecalis
2. E. faecium

A

S.K.A.P.E = To watch out organisms in
cultures; “super bombs”; drug resistant

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20
Q

resistance to rifampicin gene

A

rpoB (RNA polymerase B gene)

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20
Q
  1. OR specimens = kapag nilalagyan ng formalin, kasi di mo maeextract yung DNA
  2. Lysed na yung cells
  3. Highly fragmented na yung nucleic acids
A

Rejected samples

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20
Q

Characterization of DNA, RNA, and protein to find and identify new organisms and to further
characterize or classify known organisms.

A

influenza virus and Sars-CoV

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21
Q
  1. Viability is not as critical for most molecular testing
  2. Quality of nucleic acids may be compromised if the specimen is improperly handled
  3. DNA and especially RNA will be damaged in lysed or nonviable cells
  4. Avoid contamination that could yield false-positive results
A

SPECIMEN COLLECTION

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22
Q

only formalinized tissue we use for DNA or RNA extraction

A

Formalin fixed paraffin embedded tissue

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23
Q

pseudoperoxidase activity in sputum with blood affects downstream application of PCR

A

TRUE

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24
Q

DNA and especially RNA will be damaged in lysed or nonviable cells because of possible release of nucleases

A

TRUE

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25
Q

component of sputum with blood that inhibits taq polymerase in PCR

A

Hemoglobin

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26
Q

PCR IS VERY POWERFUL, but it can saturate the process if very small amount of DNA is used

A

TRUE

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27
Q

LLOD - Lower limit of detection

A

amount of DNA used; low LLOD is good! mas sensitive

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28
Q

Principle: Real-time monitoring of PCR progression was performed using fluorescence signal accumulation

A

Quantitative PCR

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29
Q
A
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30
Q

Principle: Isothermal Amplification was performed using four specific primers in the presence of Bacillus

A

Loop-mediated Isothermal Amplification

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31
Q

Principle: Amplification reactions were performed for individual nucleic acid molecules in a separate space

A

Digital PCR

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32
Q

Principle: The different melting temperatures of mononucleotides lead to different melting curves

A

High-resolution Melting

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33
Q

Applicability: Routine quantitative detrection of common pathogens such as novel coronavirus, HBV, human papillomavirus, and others in the laboratory

A

Quantitative PCR

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34
Q

Applicability: Absolute quantification of low-content pathogens such as HBV, HIV, and MTB, etc.

A

Digital PCR

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35
Q

Applicability: Genotyping of pathogens such as Escherichia coli, Staphylococcus aureus, adenoviruses, etc.

A

High-resolution Melting

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36
Q

Advantage: Absolute quantification, low sample requirement, and high tolerability

A

Digital PCR

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37
Q

Applicability: Primary field screening of pathogens such as MTB and Plasmodium.

A

Loop-mediated Isothermal Amplification

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38
Q

Advantage: Good specificity, high sensitivity, high degree of automation, and low cost.

A

Quantitative PCR

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39
Q

Advantage: Rapid, high throughput, short time, and low cost

A

High-resolution Melting

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40
Q

Limitations: Numerous interference factors, time-consuming, instruments are expensive

A

Quantitative PCR

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40
Q

Limitations: High cost, limited throughput, complex operation

A

Digital PCR

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41
Q

Advantage: Low instrument requirements, fast reaction speed, low cost, and high sample

A

Loop-mediated Isothermal Amplification

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42
Q

Limitations: Complex primer design, non-specific amplification, low throughput

A

Loop-mediated Isothermal Amplification

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42
Q

Limitations: High requirement for uniformity of temperature and primer design

A

High-resolution Melting

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43
Q

False-positives: Nucleic acid contamination, non-specific amplification

False-negatives: Inhibitors, enzyme inactivation, too little template

A

Quantitative PCR

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44
Q

False-positive: Nucleic acid contamination

A

Digital PCR

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45
Q

False-positive: Non-specific amplification

A

High-resolution Melting

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46
Q

False-positive: Cross-contamination

A

Loop-mediated Isothermal Amplification

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47
Q

Best dye?

A

HRM

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48
Q

HRM > Evagreen > SyBr Green 1

A

TRUE

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49
Q
  • Negative derivative in fluorescence and temperature, dalawang peaks ang nakita, edi HRM daw siya
  • Means 2 targets yung naamplify mo
  • If white peak = naamplify and may nonspecific amplification
A

TRUE

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50
Q

Polycythemia vera gene

A

JAK2 (V671E to V617F)

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51
Q

PCR (RT,qRT etc)
DNA Sequencing
Pulse Gel
Electrophoresis
MALDI TOF (mass spectrometry principle)

A

Molecular methods

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52
Q
  • PCR-based amplification.
  • can overcome low sensitivity to improve the specificity of conventional phenotypic tests.
  • provide early diagnosis for proper treatment with potential reduction in mortality and morbidity.
  • all PCR assays have been designed to detect a low load of a given microorganism among a huge number of human cells.
A

NUCLEIC ACID AMPLIFICATION TECHNIQUES

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53
Q

for MTB/RIF, MRSA, HBV, HIV, HCV, CT/NG (Chlamydia and Neisseria), HPV, SARS-CoV-2, C. difficile, etc.

A

Cepheid GeneXpert® Systems

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54
Q

Most significant sexually transmitted HPV is 16 and 18

A

TRUE

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55
Q

<100 CFU/mL = cannot be detected

A

TRUE

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56
Q

for respiratory, gastrointestinal and cerebrospinal organisms

A

BIOFIRE® FILMARRAY® SYSTEMS

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57
Q

for HIV, HBV and HCV

A

Roche COBAS® TaqMan® viral loading systems

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58
Q

Detects through electrophoresis

A

Seegene AnyplexII HPV HR Detection

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59
Q
  • Conserved regions are ideal primer targets for amplification from all bacterial species.
  • Measuring the degree of divergence observed within the 16S rRNA molecule.
  • It contains well contained regions and variable regions
  • The signature sequence obtained is compared to a database containing sequences of known microorganisms.
  • The number of similar nucleotide bases between sequences is used to calculate the percent identity and ascertain the identification of the microorganism.
A

DIAGNOSIS WITH SEQUENCING

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60
Q
  • The rRNA genes and their intergenic regions found in bacteria are commonly used for prokaryotic phylogenetic studies.
  • The small-subunit rRNA molecule is a fragment with a sedimentation coefficient of 16S and is encoded by a roughly 1542-bp gene.
  • 16S is also used for community analysis = gold standard
A

TRUE FOR DIAGNOSIS WITH SEQUENCING

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61
Q

(beta subunit of RNA polymerase)

A

rpoB

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62
Q

(manganese-dependent superoxide dismutase)

A

sodA

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63
Q

(elongation factor Tu)

A

tuf

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64
Q
  • rpoB (beta subunit of RNA polymerase)
  • sodA (manganese-dependent superoxide dismutase)
  • gyrA or gyrB
  • tuf (elongation factor Tu)
  • recA
  • secA
  • Heat shock proteins.
A

Other DNA targets have been used to better separate closed related species include:

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65
Q

Similar to 16S rRNA gene, these alternative DNA targets have conserved regions flanking variable regions that can be used to differentiate closely related bacterial species.

A

TRUE

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65
Q

● Bartonellae Species
● Borrelia Species
● Chlamydia trachomatis
● Clostridium difficile
● Mycoplasma pneumoniae
● Rickettsia Species
● Staphylococcus aureus
● Streptococcus pneumonia
● Streptococcus pyogenes
● Streptococcus agalactiae
● ^^Staph and Strep hindi masyado common

A

DETECTION OF BACTERIAL PATHOGENS

65
Q

COMMONLY USED PCR TARGETS FOR DETECTION OF Bartonella spp.

A
  1. Molecular Characterization of Isolates from Cultures
  2. Direct Molecular Detection
66
Q
  • mtRNA ssrA
  • 16S-23S Internal transcribed spacer (ITS)
  • β-subunit of RNA polymerase rpoB
A

Direct Molecular Detection via real-time PCR

67
Q
A
68
Q
  • Citrate synthase gltA
  • β-subunit of RNA polymerase rpoB
  • 16S-23S Internal transcribed spacer (ITS)
  • 16S ribosomal RNA gene 16S
  • Riboflavin synthase ribC
  • NADH dehydrogenase gamma subunit nuoG
  • Cell division protein ftsZ
  • Heat shock protein groEL
A

Molecular Characterization of Isolates from Cultures via conventional PCR

NADH - conventional PCR/RT-qPCR

69
Q

Sample in MALDI-TOF _______ while in PCR it is ________

A

pure colony; raw sample

70
Q

● PCR provides a valuable diagnostic approach in
acutely ill patients.
○ This overcomes the poor sensitivity of
microscopy and can be used either to
diagnose relapsing fever borreliosis or to
further characterize the infecting spirochete.
● Recently applied techniques include NGS and proteomic approaches.
● Not commonly assayed in the PH

A

BORRELIA SPECIES

71
Q

Molecular genotyping of ompA can be performed by using restriction fragment length polymorphism on PCR products from culture isolates, but also directly from clinical specimens.

A

CHLAMYDIA TRACHOMATIS

72
Q

The nine polymorphic membrane protein genes, pmpA to pmpI, can be used for typing but the discriminating capacity is limited.

A

CHLAMYDIA TRACHOMATIS

73
Q

The highly conserved genome of C. trachomatis can be used for multilocus target systems.

A

TRUE

74
Q

Analysis of variable numbers of tandem repeats in three loci combined with ompA sequencing can bring a significantly higher diversity index than by using ompA alone.

A

TRUE

75
Q

real-time PCRs targeting the ______ toxin genes: tcdA, tcdB and tcdC117.

A

CLOSTRIDIUM DIFFICILE

76
Q

Multiplex PCR for the detection of tcdA, tcdB, and the binary toxin (cdtA/cdtB) gene
○ one-step, rapid, and specific screening
method
○ This toxin gene profiling can allow an
evaluation of the pathogenic potential of ____

A

CLOSTRIDIUM DIFFICILE

77
Q

Isothermal helicase-dependent amplification for the detection of toxigenic ______

A

CLOSTRIDIUM DIFFICILE

78
Q

Development of pseudomembranous colitis

A

CLOSTRIDIUM DIFFICILE

79
Q

Both conventional and real-time NAATs have been used to detect ________ RNA.
- monoplex and multiplex format

A

MYCOPLASMA PNEUMONIAE

80
Q

LAMP assay also has been applied to detect M.
pneumoniae in clinical specimens using P1 sequences for primers in direct comparison to real-time PCR.

A

TRUE

81
Q

A multiplex real-time PCR assay can be used to detect point mutations in all three positions of the 23S rRNA gene (___, ____, and ____) that are related to the macrolide resistance on all clinical samples that are positive for M. pneumoniae in the repMp1 real-time PCR assay.

A

2063, 2064, 2617

82
Q

Specimen:
- Whole Blood/
- Buffy coat
- Serum/ Plasma
- Skin/eschar biopsy and autopsy organ tissue
- Eschar Swab
- Formalin-fixed tissue; paraffin-embedded tissue

A

RICKETTSIA SPECIES

83
Q

Preservation and Transportation for Rickettsia is -20°C; >24hrs, EXCEPT:

A

Eschar Swab: -2-8°C; >24hrs
Formalin-fixed: Room Temperature

84
Q

a leading cause of bone and joint infections and one of the most common causative pathogens of bacterial pneumonia in children.

A

STAPHYLOCOCCUS AUREUS

85
Q

____ and ___ are the main genes responsible for the resistance of MRSA to most of the β-lactam antibiotics.

A

mecA and mecC

86
Q

PCR is considered to be the best molecular diagnostic tool for MRSA detection.

A

TRUE

87
Q

Duplex PCR assay detecting mecA and ____ genes can be very useful.

A

femB/nuc

88
Q

A triplex PCR targeting 16S rRNA, mecA, and nuc genes can reach 98% accuracy within 6h of visible growth detection.

A

TRUE

89
Q

Pneumococcal surface adhesion A (psaA), pneumolysin (ply), penicillin-binding protein (PBP), and autolysin (lytA)

A

STREPTOCOCCUS PNEUMONIAE

90
Q

Real-time PCR: Analyzing sputum through real-time PCR with the targets at lytA.

A

STREPTOCOCCUS PNEUMONIAE

91
Q
  • GASDirect test identifies specific rRNA sequences of S. pyogenes in pharyngeal specimens by a single-stranded chemiluminescent nucleic acid probe
  • Can be applied for primary testing, has been used as a backup test to negative antigen tests, and is suitable for batch screening of throat cultures.
A

STREPTOCOCCUS PYOGENES

92
Q

Specimens used:
- vaginal-rectal swabs, amniotic fluid, neonatal
screening swabs, blood, breast milk, urine,
and serum.

A

STREPTOCOCCUS AGALACTIAE

93
Q
  • LAMP Method can amplify target nucleotide sequences at isothermal conditions (usually 60-65°C) within 90 mins by using four or six primers.
  • Amplification can be detected by macroscopic observation of turbidity or color change of a fluorescent dye.
A

STREPTOCOCCUS AGALACTIAE

94
Q

Developed successfully by using probes targeting cfb gene.

A

STREPTOCOCCUS AGALACTIAE

95
Q

Universal 16S PCR also has been used to identify GBS (Group B Streptococcus) from blood, bone, and joint infections.

A

TRUE

96
Q

Targets for GBS-PCR include:
sip gene - codes for the Sip immunogenic protein.
cfb gene - codes for the Christie-Atkins-Munch-Petersen factor.
scpB gene - codes for the C5a peptidase
ptsI gene - codes for phosphotransferase.

A

TRUE

97
Q

codes for the Sip immunogenic protein

A

Sip gene

98
Q

codes for the Christie-Atkins-Munch-Petersen factor

A

cfb gene

99
Q

codes for the C5a peptidase

A

scpB gene

100
Q

codes for phosphotransferase.

A

ptsI gene

101
Q

For differentiation between strains of the same fungal species, multilocus sequence typing of housekeeping genes can be used.

A

TRUE

102
Q

PCR-based DNA amplification or ______

A

isothermal amplification

103
Q

Genus or species-specific primers and probes methods:
- Southern blotting, slot blotting, PCR-enzyme immunoassay microarray, nested PCR, PCR-restriction fragment length polymorphism, and microsatellites

A

TRUE

104
Q

Nested PCR can be used to detect Aspergillus and Candida.

A

TRUE

105
Q

Tissue is processed frequently for histopathology with FFPE tissue, which hampers the molecular identification workflow because of technical issues.

A

TRUE

106
Q

Fresh frozen tissue gives a better yield than FFPE tissue in qPCR detection.

A

TRUE

107
Q

Target Gene: Actin

A

Aspergillus

108
Q

Target Gene: β-Tubulin

A

Phaeacremionium
Aspergillus
Pseudallescheria
(PAP)

109
Q

Target Gene: Calmodulin

A

Aspergillus
Pseudallescheria
(AP)

110
Q

Target Gene: Chitin synthase 2

A

Lacazia loboi

111
Q

Target Gene: Cytochrome b

A

Aspergillus
Trichosporon
Rhodotorula
(ATR)

112
Q

Target Gene: D1-D2

A

Most fungi

113
Q

Target Gene: Elongation factor 1a

A

Fusarium species

114
Q

Target Gene: ITS

A

Medically significant yeasts
Fungi

115
Q

Target Gene: 26S

A

Medically relevant Fusarium and Scedosporium

116
Q

For differentiation between strains of the same fungal species, multilocus sequence typing of house-keeping genes should be used.

A

TRUE

117
Q

For direct sequencing, the ___ and ___ fragments can be used for PCR amplification.

A

26S and 28S

118
Q

_______ is highly sensitive and specific for the detection of Aspergillus DNA or RNA.

A

NAAT

119
Q

Real-time PCR can be used to quantify fungal burden

A

TRUE

120
Q

Isothermal amplification techniques, such as nucleic acid sequence-based amplification (NASBA), detect Aspergillus nucleic acids

A

TRUE

121
Q

In situ hybridication (ISH) probes targeting fungal rDNA have been used for the detection of Aspergillus in fresh and FFPE tissues without requiring nucleic acid extraction or amplification. This enables?

A

enables direct visualization of organisms with the use of labeled probes that bind to complementary fungal sequences.

122
Q

rDNA gene cluster: most common target of assays designed for direct detection in clinical specimens because of the presence of highly conserved (18S rDNa and 28S rDNA) and variable (ITS and D1/D2) regions.

A

TRUE

123
Q

Genus level assay designs often target ____

A

18S

124
Q

A. fumigatus-specific assays target ITS-1, mitochondrial DNA, alkaline protease, or Aspergillus collagen-like (acl) genes.

A

TRUE

125
Q

A novel, simple real-time qPCR use a probe as a primer to initiate PCR amplification under the high fidelity (HF) DNA polymerase and the emitted fluorescence during the amplification can be monitored during a real-time PCR amplification.

A

DIAGNOSIS OF HUMAN IMMUNODEFICIENCY VIRUS INFECTION

126
Q

Tolerance to mismatches between primer/probe and target and the one primer-one HF man probe system simplifies the method, improves the sensitivity and accuracy.

A

DIAGNOSIS OF HUMAN IMMUNODEFICIENCY VIRUS INFECTION

127
Q

_______________-mediated qPCR method is a simple, sensitive, and promising approach for the diagnostics for viral infectious diseases.

A

HF DNA polymerase-mediated qPCR method

128
Q
  • Some HPV types have the potential to cause lesions that progress to cancer.
  • The highest risk for cancer development occurs as a result of prolonged persistent infection over many years.
A

TRUE

129
Q

The majority of molecular diagnoses are designed to detect nucleic acids of the 12 IARC HPV group 1 carcinogens

A

HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, and 59

130
Q

Multiplex real-time PCR and nucleic acid hybridization with four different fluorescent reporter probes can be used to concurrently detect the L1 gene of HPV16 and HPV18 as individual reactions and HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, and -68 as a pooled result.

A

TRUE

131
Q

L1 gene of HPV16 and HPV18 as ____ reactions

A

individual

132
Q

HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, -66, and -68 as _____ result

A

pooled result

133
Q

Detection of HPV E6/E7 oncogene mRNA in cervical cells is an alternative to detection of HPV DNA.

A

TRUE

134
Q

HPV tests based on nucleic acid sequence-based amplification (NASBA) can detect very little expression of E6/E7 mRNA for transient infection.

A

TRUE

135
Q

Persistent infections = overexpression of _____

A

E6/E7 mRNA

136
Q

__ refers to dominant promoter

A

P97

137
Q

All PVs are similar in their genetic organization and appearance under electron microscope.

A

TRUE

138
Q

URR

A

Upstream Regulatory Region

139
Q

Real-time PCR is one of the latest techniques frequently used to diagnose viral hepatitis.

A

TRUE

140
Q

PCR-based assays, coupled with oligonucleotide microarray technology, allow for the simultaneous detection and genotyping of several viruses, including blood borne pathogens, respiratory viruses, and adenoviruses.

A

TRUE

141
Q

Multiplex qPCR assays use the most conserved region representing all the strains/variants for detection of the hepatitis viral genome in body fluid.

A

TRUE

142
Q

Multiplex qPCR has been employed successfully for the simultaneous detection of hepatitis virus A, B, C, D, and E and genotyping of their strains.

A

TRUE

143
Q

A single-step multiplex qPCR assay allows for an early diagnosis and timely treatment of patients with viral hepatitis.

A

TRUE

144
Q

HAV Virus, HCV, HGV

A

5’ UTR

145
Q

HBV

A

S and X gene

146
Q

HDV

A

Ribozyme-1

147
Q

HEV

A

ORF2 and ORF3

148
Q

Segment __ is complementary to the HBV DNA plus strand from nt 1615 to nt 1604

A

A

149
Q

Segment __ is consensual to the HIV long terminal repeat (LTR) region, which differs from the HBV DNA sequence

A

B

150
Q

To reduce rcDNA contamination: a chimeric sequence composed of two segments to increase specificity: Segment A and Segment B

A

TRUE

151
Q

Can effectively distinguish cccDNA from other HBV DNa

A

TRUE

152
Q

______ is regarded as the best test for quantitative cccDNA detection.

A

Southern Blotting

153
Q

The higher the mass, the longer the time of flight of the ion.

A

TRUE

153
Q

A peptide is placed on a matrix, which causes the peptide to form crystals

Laser pulse is used to excite the chemical matrix, creating a microplasma that transfers the energy to protein molecules in the sample, ionizing them and ejecting them into the gas phase.

Protein molecules that have packed up a single proton can be selected by the MS for mass analysis.

A

TRUE

153
Q

The general procedure for the identification of bacteria and yeast by MALDI-TOF MS using the intact-cell method

A

TRUE

154
Q

● 16S rRNA gene
● 16S-23S ITS (locus)
● gltA (citrate synthase)
● rpoB (β-subunit of RNA polymerase)
● ribC (riboflavin synthase)
● nuoG (NADH dehydrogenase gamma subunit)
● ftsZ (cell division protein)
● groEL (heat shock protein)
● ssrA (transfer-messengerRNA)

A

Bartonellae spp

154
Q

● ompA
● pmpA - pmpl

A

Chlamydia trachomatis

155
Q

● 16s rRNA gene (commonly targeted;
broad-range)

A

Borrelia spp

156
Q

● tcdA
● tcdB
● tcdC117
● Binary toxin (cdtA/cdtB) gene

A

Clostridium difficile

157
Q

● P1 sequences
● 23S rRNA gene (positions 2063, 2064 and 2617)
● repMp1

A

Mycoplasma pneumoniae

158
Q

● 16s rRNA gene (commonly targeted; broad-range)
● 17kDa antigen gene

A

Rickettsia spp

159
Q

● mecC gene
● 16s rRNA
● mecA gene
● Nuc genes
^^last 3 in triplex PXR = 98% accurate

A

Staphylococcus aureus

160
Q

● psaA (Pneumococcal surface adhesion A)
● ply (pneumolysin)
● PBP (penicillin-binding protein)
● lytA (autolysin)
○ ^^Sputum real time-PCR

A

Streptococcus pneumoniae

160
Q

● 16s rRNA gene (commonly targeted; broad-range)
● emm gene

A

Streptococcus pyogenes

161
Q

● 16s rRNA gene (commonly targeted; broad-range)
● sip gene (Sip immunogenic protein)
● cfb gene (Christie-Atkins-Munch-Petersen factor)
● scpB gene (C5a peptidase)
● ptsI gene (phosphotransferase)

A

Streptococcus agalactiae

162
Q

● Actin
● rDNA gene cluster
● 18S
● ITS-1
● Mitochondrial DNA
● Alkaline protease
● acl genes
^^ last 3 (A. fumigatus-specific)

A

Aspergillus

162
Q

● L1 gene
● E6/E7 oncogenes

A

Human Papillomavirus

163
Q

● Conserved regions of the viral genome (see
table below)
● cccDNA (for HBV)

A

Hepatitis virus

MOLBIO LEC (1 decks)

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